On Mon, Feb 1, 2016 at 11:15 PM, Prayagraj Fandilolu <fprayagraj.gmail.com>
wrote:
> Dear Amber users,
>
> I am simulating a RNA system using the ff14SB in Sander. I am facing an
> issue with SP3 planar nitrogen atoms of my system. After minimization, the
> orientation of planar SP3 Nitrogen is changing and its planar conformation
> is lost.
>
> I have checked the same system with older ff99bsc0. This ff works fine and
> the SP3 planar nitrogen atoms are still planar after minimization.
>
> I am not getting a clue into this...
>
> can some one give me a solution to this issue????
>
> Other parameters being loaded with ff14SB are:
>
> frcmod.modrna08
> frcmod.chiOL4
>
I'm not sure why you are loading these. The manual describes what force
field each leaprc contains. Since you seem to be (??) loading extra
parameters aside from what is loaded inside each leaprc itself, you are
*not* actually using ff14SB here.
> frcmod.ionsjc_tip3p
>
Loading ion parameters is necessary, as you've done here.
>
> while in case of ff99bsc0 i am using:
>
> leaprc.rna.ff99
> leaprc.ff99bsc0
> frcmod.ol.dat
>
Same comments above. leaprc.ff99bsc0 (now located in
oldff/leaprc.ff99bsc0) is the full specification of that force field.
The "extra" parameters you loaded may have been overwriting "good"
parameters with bad ones.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 02 2016 - 04:30:03 PST
